SITC 2018

Ready. Checkpoint. GO.

Get a head start with the expanded Advanta IO Gene Expression Workflow.

Feature

Gene expression profiling of the tumor microenvironment has proven effective in measuring immune response during research in cancer progression and therapeutic response. Preconfigured quantitative PCR (qPCR) panels containing hundreds of gene targets represent a potential solution, but can require significant time and resources to implement in the laboratory and can be difficult to customize for specific experimental needs.

The Advanta™ IO Gene Expression Assay workflow was designed to meet this need, detecting 170 gene expression markers involved in checkpoint therapeutic response. Ideal for accelerating the identification of potential predictive biomarker signatures of checkpoint immunotherapeutic response, the Advanta IO Gene Expression Assay was developed in collaboration with leading researchers from academia and biopharma to provide the right balance of biomarker breadth, assay flexibility and workflow efficiency.

As an expanded workflow solution, we now offer an optimized Advanta FFPE RNA Extraction Kit, which produces high-quality RNA from precious tumor samples and improves the sensitivity of tumor transcript detection. As an added benefit, a synthetic template representing the amplification targets of all 170 genes is also available as a positive control. When using this new kit and control together with the Advanta IO Gene Expression Assay on the Biomark™ HD system, researchers can accurately assess 24 to 96 tumor samples at a time with high confidence and efficiency.

Completing the workflow, the GO Immuno-Oncology Workbench was developed by GenomOncology to provide powerful, flexible and intuitive analysis of immuno-oncology datasets. Now available from Fluidigm, the GO Immuno-Oncology Workbench enables researchers to unlock new clinical insights from translational immuno-oncology studies, including the identification of meaningful gene expression biomarkers that correlate with therapeutic response.

“The GO Immuno-Oncology Workbench is a powerful software tool that enables comprehensive analysis of immuno-oncology cohorts, integrating molecular and phenotypic data together with immuno-oncology-specific annotations to power translational studies,” said Manuel Glynias, CEO of GenomOncology. “We are excited to see the new insights uncovered using this comprehensive approach, which we we offer in conjunction with Fluidigm to empower the growing immuno-oncology community.”

“Fluidigm is the partner of choice within the immuno-oncology research community, enabling deep interrogation of the tumor microenvironment and immune response with mass cytometry,” said Chris Linthwaite, President and CEO of Fluidigm. “In partnership with GenomOncology, we are expanding our immuno-oncology gene expression offering to the cancer community with a full microfluidics-based workflow solution from RNA extraction to data analysis. By providing a comprehensive view of tumor immunity, utilizing microfluidics and mass cytometry technologies, we are empowering researchers to uncover unique health insights that could transform the future of cancer care.”

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Deciphering T Cell Diversity in the Tumor Microenvironment

Evan Newell on decoding immune cell heterogeneity with mass cytometry

Spotlight

Understanding the full complexity of the immune system and its response to infections and diseases, especially in cancer, has eluded researchers for decades. Whether analyzing blood or tissue samples, investigators have struggled to categorize the heterogeneity found in the T cell composition of different tumors.

In a recently published paper in Nature, Evan Newell, PhD, and colleagues identify a potential biomarker of tumor-antigen specificity and provide a new perspective on the heterogeneity of T cells in the tumor microenvironment. Newell led this research as a principal investigator at the Singapore Immunology Network (SIgN). First author Yannick Simoni, PhD, formally a senior research fellow at Singapore’s Agency for Science, Technology and Research (A*STAR), accumulated data for more than 140 different tumor samples from patients with lung and colorectal cancer to search for correlations between this heterogeneity and various characteristics of the patient samples.

“CyTOF technology has a really unique niche for interrogating the tumor microenvironment,” said Newell. “It has relatively high throughput and high dimensionality, allowing us to open up a lot of doors.”

Newell’s lab developed novel approaches for identifying and characterizing antigen-specific T cells. In this paper, his group used MHC tetramer staining in conjunction with mass cytometry for in-depth analysis of cellular phenotype and function.

His group and others “have been stuck on saying, ‘It’s crazy. There are so many different types of immune cells.’ And you can use all kinds of fancy analyses to show that it’s very diverse,” Newell said. “But we’ve taken it a little bit further by getting to some simple correlates of clinical states.”

Newell and his team used mass cytometry that relies on time-of-flight mass spectrometry (CyTOF® technology) to simultaneously assess antigen specificity and deep phenotypic characteristics of T cells. The resulting data shows that T cell populations infiltrating lung and colorectal tumors may be specific for tumor antigens or for a wide range of epitopes unrelated to cancer, such as viral antigens. Moreover, he discovered that these bystander T cells have diverse phenotypes that overlap with tumor-specific cells and lack CD39 expression.

CD39: A more accurate marker of tumor antigen specificity

Newell and Simoni’s discovery of a more accurate marker for tumor antigen specificity relied on a multiplexed approach that allowed them to simultaneously profile T cells within the tumor microenvironment for phenotype and function. Instead of focusing only on tumor-reactive cells, the team looked at all antigen-specific T cells and was able to identify cancer-unrelated antigen-specific T cells in tumors.

“We found a few examples of tumor-specific T cells, and then we also had examples of T cells specific for cancer-unrelated antigens, like the flu and Epstein-Barr virus. This was key in trying to interpret what all this heterogeneity meant,” Newell said.

The next step was to determine what was different about the non-cancer-specific T cells. Simoni observed that many of them expressed what typically have been identified as tumor-infiltrating T cell markers, such as CD69 and PD-1, which may have a role in tumor reactivity.

“The striking thing was that we saw hardly any expression of CD39, which is known as being immunosuppressive,” he said.

Since their findings showed that the tumor-specific T cells expressed CD39, Simoni could build a case for CD39 as a more accurate marker of tumor antigen specificity. Newell now believes CD39 also could be useful as a predictor of response to checkpoint blockade, and as a starting point for the development of novel therapeutics.

Advantage to using CyTOF technology for immune cell profiling

Newell started using mass cytometry for studying human T cell response as a postdoctoral student at Stanford University more than six years ago. He attributes much of his success to the technology’s ability to simultaneously look at many phenotypic markers and antigen specificity, allowing his team to better understand the number of distinct cellular phenotypes and how they are related to each other.

In the Nature paper described here, Newell also used whole transcriptome RNA-seq to validate his mass cytometry findings. He believes the two techniques make a powerful combination for identifying new markers associated with specific cell populations. However, Newell explains that compared to RNA-seq, mass cytometry “can more accurately measure protein and do it on a larger number of cells, which gives a much higher resolution when describing cellular heterogeneity.”

CyTOF applications beyond cancer research

Newell’s ultimate goal is to gain a better understanding of how the human immune system works, and he thinks the best way to accomplish this is by searching for co-variations.

“Mass cytometry is especially great for that because it’s really improving our understanding of immune system variation in humans,” Newell said. “It has also been excellent for mapping out trajectories of cellular development.”

In addition to providing cutting-edge technology platforms to researchers, SIgN aims to support Singapore biotechnology companies such as Newell’s spinoff immunoSCAPE, which provides antigen-specific T cell screening and profiling services. Newell, who established his lab at SIgN in 2012, has moved to the Fred Hutchinson Cancer Research Center in Seattle as part of the Vaccine and Infectious Disease Division. His lab will continue to investigate antigen-specific T cells in cancer and other diseases. He also has been working on developing computational approaches to improve analysis of these large datasets.

Beyond cancer research, Newell and colleagues are using mass cytometry to study a variety of topics from myeloid cell composition in dendritic cell development to T cell antigen specificity in viruses such as hepatitis B and dengue. By taking a multiplexed approach in investigating the phenotype and function of cells from different viral disease stages, Newell’s team can assess the use of T cell phenotypes as future biomarkers for patient outcomes.

“CyTOF technology has a really unique niche for interrogating the tumor microenvironment,” said Newell. “It has relatively high throughput and high dimensionality, allowing us to open up a lot of doors.”

Fluidigm Products are for Research Use Only. Not for use in diagnostic procedures.

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Quality RNA Means Better Cancer Research

Advanta IO Gene Expression Assay

Tumor gene expression profiling in cancer research is an effective tool for measuring immune response during cancer progression and treatment studies. As emerging therapies reveal new biomarkers and expand the need for sample testing, the costs and labor required to complete this important work also increase.

Cancer researchers now have a reliable, sensitive and cost-effective tool for identifying gene expression signatures from immune and cancer cells: The Advanta™ IO Gene Expression Assay is designed for use with the Biomark™ HD system. For optimized gene detection, pair it with the Advanta™ FFPE RNA Extraction Kit.

Improving the process

Processing FFPE samples can be challenging due to limited sample quantities or fragmented RNA transcripts caused by nucleic acid degradation as a result of tissue fixation and storage methods. In addition, most extraction kits rely on column purification to remove RNA and DNA, causing significant nucleic acid loss during the isolation process. To address this issue, the Advanta FFPE RNA Extraction Kit uses a column-free approach to effectively recover quality RNA from FFPE samples.

Download our product flyer to learn more about using the Advanta FFPE RNA Extraction Kit to accelerate your investigative research.

“Sirona Dx specializes in expression profiling of challenging FFPE samples and we welcomed the opportunity to partner with Fluidigm to develop an improved RNA extraction methodology. To date we have processed several hundred samples with the Advanta FFPE RNA Extraction Kit, and our pharma clients have been astonished by the quality of RNA extracted and delighted at our ability to interrogate more of their precious FFPE samples.”
—Nasry Yassa, CEO, Sirona Dx

Sirona Dx case study

Clinical research services provider Sirona Dx, Inc., based in Vancouver, Washington, performed gene expression analysis of FFPE samples extracted using the Advanta FFPE RNA Extraction Kit and a leading column-based commercial kit. After extraction, the group reverse-transcribed and preamplified the RNA and analyzed the cDNA on Biomark HD using the Advanta IO Gene Expression Assay panel containing 170 unique biomarkers for profiling tumor immunobiology and identification. Gene expression analysis data demonstrated more target gene detection in samples extracted using the Advanta FFPE RNA Extraction Kit. These samples typically showed lower cycle threshold values than those extracted using the alternative kit.

“Sirona Dx specializes in expression profiling of challenging FFPE samples and we welcomed the opportunity to partner with Fluidigm to develop an improved RNA extraction methodology,” said Sirona Dx CEO Nasry Yassa. “To date we have processed several hundred samples with the Advanta FFPE RNA Extraction Kit, and our pharma clients have been astonished by the quality of RNA extracted and delighted at our ability to interrogate more of their precious FFPE samples­.”

Webinar | Understanding the Immune Composition

Hear Dr. Kurt Schalper describe how research performed at the Translational Immuno-Oncology Laboratory at Yale Cancer Center uses Imaging Mass Cytometry™ (IMC™) as one way to open new opportunities for biomarker discovery and identification of targets that can lead to patient selection for novel immunostimulatory therapies.

In this recorded webinar, Schalper discusses:

how his group deciphers the tumor microenvironment and its role in immuno-oncology using highly multiplexed panels

Please join us for the webinar and an in-depth Q&A session that follows.

Dr. Schalper is currently Assistant Professor of Pathology and the Director of the Translational Immuno-Oncology Laboratory at the Yale Cancer Center. The Translational Immuno-Oncology lab is devoted to producing and supporting high-quality translational research in immuno-oncology through standardized analyses of biomarkers and cross-integration with other Yale resources.

Power a new future in molecular pathology

When interrogating tissue sections for protein markers, standard immunohistochemistry methods fall short by allowing only a few proteins to be detected at a time. Similarly, the increasing demands for greater efficiency and automation in genetic assay pipelines are common challenges in the molecular laboratory.

At Fluidigm, we have embraced these challenges. This year we will feature products that will empower you to significantly expand the number of proteins you can detect on each slide with Imaging Mass Cytometry™ and bring greater cost efficiency and automation to your targeted NGS library prep pipeline.

Visit Fluidigm at Booth 1800

Meet us in San Antonio to explore how our exciting products can empower your translational and clinical research programs.

Exhibit Dates and Hours

Thursday, November 1

11:30 am–4:30 pm
5:45–7:00 pm (welcome reception in Exhibit Hall)

Friday, November 2

9:00 am–4:00 pm

Saturday, November 3

9:00 am–1:30 pm

Featured Products

Hyperion Imaging SystemThe Hyperion™ Imaging System enables you to comprehensively interrogate complex cellular phenotypes and their interrelationships in the context of the tumor microenvironment with Imaging Mass Cytometry™.

At Fluidigm, we enable comprehensive cellular and molecular profiling of the immune system and the tumor microenvironment with proven mass cytometry, Imaging Mass Cytometry™ (IMC™) and automated microfluidics solutions.

Whether you seek to target new biomarkers and pathways or to optimize the effectiveness of checkpoint inhibitors, CAR T cells or cancer vaccines, Fluidigm can help you identify new insights to reach your next research breakthrough.